Men wearing Russian-marked military uniforms reportedly blocked Belbek international airport in Sevastopol in the capital of Ukraine's strategic Crimea region early on Friday.
Interfax news agency has reported that armed persons, dressed in camouflage, remained on the premises of the airport.
BBC News said that Russia's Black Sea Fleet has denied the involvement of Russian servicemen.
Ukraine Interior Minister Arsen Avakov has said that unidentified men were patrolling other main Crimean airport, Simferopol, which serves the regional capital.
In a Facebook post Avakov wrote: "I can only describe this as a military invasion and occupation."
The situation at the Simferopol airport has returned to near-normalcy, with flights landing and departing on schedule.
In an interview with Ekho Moskvy radio station, a Simferopol airport spokesman said: "They thought that protest forces had landed there, but when they saw for themselves that there was no one there, they apologized and left."
According to a few other reports, the protest forces wanted to prevent Avakov and Ukrainian Security Council head Valentyn Nalyvaichenko from arriving in Crimea.
These developments can be traced back to Ukraine's ousted president Viktor Yanukovych's decision to sever ties with Europe for a bailout loan from Russia.
Russia has reportedly given asylum to Yanukovych, following the recent protests in Ukraine capital Kiev.
The Autonomous Republic of Crimea region was transferred by Russia to Ukraine in 1954, and is dominated by ethnic Russians.